MolNFT v1 · #15928 · protein + RNA
The crystal structure of the 50S large ribosomal subunit from deinococcus radiodurans complexed with a tRNA acceptor stem mimic (asm) and the antibiotic sparsomycin
1NJM · 23S ribosomal RNA: “The crystal structure of the 50S large ribosomal subunit from deinococcus radiodurans complexed with a tRNA…”. X-ray diffraction, 2 ligands (PPU, SPS), 20 pockets (best druggability 0.86). MolNFT v1 #15928 on…
- PDB
- 1NJM
- Type
- protein + RNA
- Length
- 3,137 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 23S ribosomal RNA; TRNA acceptor stem mimic; 50S ribosomal protein L16; General stress…
- UniProt
- Q9RXJ5, Q9RX88
- Ligands
- PPU, SPS
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 0% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 0 | 23S ribosomal RNA | rna | 2766 | — | — |
| 5 | TRNA acceptor stem mimic | rna | 24 | — | — |
| K | 50S ribosomal protein L16 | protein | 124 | 0% helix, 0% strand | Q9RXJ5 |
| T | General stress protein ctc | protein | 223 | 0% helix, 0% strand | Q9RX88 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 923 | 0.86 | 0.89 | 81 | empty |
| 2 | 1082 | 0.85 | 0.88 | 71 | empty |
| 3 | 773 | 0.85 | 0.90 | 63 | empty |
| 4 | 1195 | 0.83 | 0.86 | 88 | empty |
| 5 | 447 | 0.81 | 0.90 | 45 | empty |
Interfaces
5 interfaces between chains.
- 0–K · 890 Ų buried · 0 hydrogen bonds · protein-nucleic
- 0–5 · 607 Ų buried · 20 hydrogen bonds · nucleic-nucleic
- 0–T · 256 Ų buried · 0 hydrogen bonds · protein-nucleic
- 5–K · 52 Ų buried · 0 hydrogen bonds · protein-nucleic
- K–T · 35 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 1NJM · The crystal structure of the 50S Large ribosomal subunit from Deinococcus radiodurans… · the same entry in another collection · chain 0 against 0, TM-score 1.00
- Q9RXJ5 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L16 (Q9RXJ5) · a predicted model of the same protein · chain K against A, TM-score 0.87
- Q9RX88 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L25 (Q9RX88) · a predicted model of the same protein · chain T against A, TM-score 0.72
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q9RXJ5
- Every structure of UniProt Q9RX88
- Elsewhere: RCSB PDB 1NJM · PDBe 1NJM · UniProt Q9RXJ5 · UniProt Q9RX88
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